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I am going to be purchasing a AppleTV shortly but am concerned with one thing. I use a Universal Remote (specifically a Harmony Remote, the H688). I am wondering if the Apple Remote using standard IR and as well if it will work with a Harmony Remote or other universal remotes?

Doubtful that your universal remote has the Apple TV codes on it. I have seen remotes though, where you hold up the remote to the universal remote and it can "memorize" IR signals from a foreign remote.

Does the Harmony have such a feature?

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OK, just updated to the latest software and looks like the AppleTV hasn't been added...yet. Though I found that it supports the Mac Mini, so it shouldn't be too difficult teaching it to work with an AppleTV seeing as how they both use the same remote and software (AppleTV is essentially Front Row with a pretty skin).

I've had a Logitech Harmony for the last 6 months, and when I initially got it, I uploaded the Apple Remote instructions to it. Worked great on my iMac and MacBook Pro and handled all the comands that the Apple remote could. Now that I have an AppleTV, I was able to include it in my theatre system and low and behold, my Harmony picked up where the AppleTV remote left off.
All the apple remotes are the same, there's nothing special about the one that comes with AppleTV. You can take that and use it on any existing (Intel) Mac and it will work just the same as the one that came with the computer.
Mine works!